So, today I came to the office just to find that my laptop had autoupdated, amongst other things, XCode which is now Version 10.2.1 (10E1001).
Having a moment of honest panic I tried to recompile the AmberTools18 package and yes, once again I cannot compile… This is not using the gnu gcc (which still, however, does not work and fails with the “_Atomic” error). This issue is still persistent and has not been fixed by the developers or by apple and diskussions are seemingly ongoing on how to handle this problem. I did exactly what worked on the last version and what is outlined in the latest confirmed install procedure on the website though it fails with the same parmed error as last time.
…
…
copying parmed/modeller/data/standard_residues.lib -> build/lib.macosx-10.7-x86_64-2.7/parmed/modeller/data
UPDATING build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py
set build/lib.macosx-10.7-x86_64-2.7/parmed/_version.py to '3.0.0+57.g74a84d30'
running build_ext
building 'parmed.amber._rdparm' extension
creating build/temp.macosx-10.7-x86_64-2.7
creating build/temp.macosx-10.7-x86_64-2.7/src
clang -fno-strict-aliasing -I/Users/guolaa/SOFTWARE/amber18/miniconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src -I/Users/guolaa/SOFTWARE/amber18/miniconda/include/python2.7 -c src/_rdparm.cpp -o build/temp.macosx-10.7-x86_64-2.7/src/_rdparm.o
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
In file included from src/_rdparm.cpp:17:
/Users/guolaa/SOFTWARE/amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error: 'locale' file not found
#include <locale>
^~~~~~~~
1 warning and 1 error generated.
error: command 'clang' failed with exit status 1
make[2]: *** [parmed] Error 1
make[1]: *** [serial] Error 2
make: *** [install] Error 2
I have commented out the libstdc++ lines as described and done a search/replace (:%s/libstdc++/libc++/g) to make sure I did not miss a new line or something else however it still does not work and fails with the same error. These are the files modified:
$AMBERHOME/AmberTools/src/configure2
$AMBERHOME/AmberTools/src/pytraj/setup.py
Are there any more files referencing the now deprecated c++ stuff from Xcode that I am unaware of?
(( Maybe it’s just time to give up and dual-boot as it at least seems that Apple is hellbent on breaking cross platform compatibility ))
Best regards
// Gustaf
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Received on Thu Apr 18 2019 - 01:30:02 PDT
